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PROFTMB(1) User Commands PROFTMB(1)

NAME

proftmb - per-residue prediction of bacterial transmembrane beta barrels

SYNOPSIS

proftmb [options]

DESCRIPTION

proftmb predicts bacterial transmembrane beta barrels from sequence using profile fed Hidden Markov Models (HMM).

Output format

Self-annotating. Letters of prediction: 'i' - inside cytoplasm, 'O' - outside cytoplasm, 'U' - up (on chain moving out of cytoplasm), 'D' - down (on chain moving into cytoplasm).

References

To invoke the menu, type:

proftmb --menu

The options are:

root path where files (options -s,-r,-l,-a,-e,-t,-u,-z,-n) reside
state reduction for decoding
state reduction for reporting
list of membrane strand states
<STRING> file containing means and sd's at integral length values
file mapping coverage and accuracy values to z-scores
background frequency file
minimum z-score for per-residue prediction
output file prefix for the three files generated: PREFIX_dat.txt, PREFIX_proftmb_pretty.txt PREFIX_proftmb_tabular.txt
data representing the model architecture
params representing the encoded training data
psiblast profile (-Q) or directory (full pathname or relative to current directory) with many profiles
if -q option points to a single file, this is the name
list of psiblast files to process in directory (leave blank to process all files)
pretty output file (overrides automatic name PREFIX_proftmb_pretty.txt)
<STRING> tabulated output file (overrides automatic name PREFIX_proftmb_tabular.txt)
<STRING> data output file (overrides automatic name PREFIX_dat.txt)
<BOOL> output version information and exit
<BOOL> be quiet

BUGS

Please report bugs at <https://rostlab.org/bugzilla3/enter_bug.cgi?product=proftmb>.

EXAMPLES

 proftmb @/usr/share/proftmb/options -q /usr/share/doc/proftmb/examples/example.Q -o /tmp/example

The above produces 3 output files: /tmp/example_proftmb_tabular.txt, /tmp/example_proftmb_pretty.txt and /tmp/example_dat.txt. Compare these to the examples in /usr/share/doc/proftmb/examples.

COPYRIGHT

Copyright © 2004 Henry Bigelow

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This package is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.

July 2024 proftmb 1.1.12